I would move the data to the HDD first, then the system to the SSD - that way you don't run out of space & can use recursive copy/move without duplicating.
The way I did this was to create a smallish partition - 15G IIRC - for boot & most of the smaller directories, around 20G for /usr, and the remainder of the SSD for /home (I tend to install lots of packages over the years!) using
gparted, and create folders for 'Stuff' on the large HDD; along the lines of
cd /path_to_3TBdrive ; mkdir Music Movies Documents... & then move out large files from my /home to the new HDD, finally copying the remainder of the system over using a live CD - you can then move the system folders while they're not mounted, re-write /etc/fstab to suit (the SSD copy of course!), put the [small enough] residue of your /home folder into the 3rd SSD partition, use grub to make the SSD boot & you're done.
There is sufficient info in askubuntu that I haven't re-written the detail on this part!